It depends what warranty work you were having done as you can always argue that they arent related. In my mind its no different to putting a new set of alloys on; thats still not an original part but changes the car from the manufacturers original. As I have said in another thread though the dealers are hit and miss - what you are told at one isn't always true at another.
You could always keep the old, standard ones and pop them back on if you ever need anything doing lol....